This is the Winfree lab DNA Circut Compiler, peppercompiler. It assists DNA programmers in building DNA computers by providing a templating language for specifying generic components and interfacing with state of the art designers and kinetic simulators to create and test sequences.
Peppercompiler can be used directly, through scripts starting with "pepper-", or can be used as a Python library, though the API should not be considered stable yet. Users of older versions should note that script names have changed.
Peppercompiler also includes, and installs, SpuriousSSM.
The Pepper Circuit Compiler was originally developed by Shawn Ligocki, with later modification by Chris Berlind, Joseph Schaeffer, Constantine Evans, and Erik Winfree.
The easiest way to install peppercompiler is via Pip:
pip install git+https://github.com/DNA-and-Natural-Algorithms-Group/peppercompiler.git
Alternatively, normal python installation methods (easy_install, setup.py) may be used. Peppercompiler is compatible with both Python 2.7 and Python 3.
Installation requires a working C compiler so that SpuriousSSM can be compiled. If compilation does not work for you, please let us know.
To use Nupack, NUPACKHOME should be set to your Nupack directory.
To use Multistrand, make sure that its executables are on your path. However, the Multistrand functionality has not recently been tested.
Run
$ pepper-compiler circuit
to compile “circuit.sys” or “circuit.comp” and produce the design specification, “circuit.pil” (use --des for .des format used by the Nupack designer).
Process “circuit.pil” with a designer. For example, to use spuriousSSM, run
$ pepper-design-spurious circuit
to produce the design, “circuit.mfe”.
Then, run
$ pepper-finish circuit
to produce a list of all sequences, “circuit.seqs” and run Multistrand on the designed sequences.
Advanced options of pepper-compiler, pepper-design-spurious and pepper-finish can
be examined by using the --help flag (e.g. python compiler.py --help).
Extended functionality:
-
You can fix certain sequences when you begin compilation
Ex:
$ pepper-compiler --fixed=circuit.fixed circuit -
You can get verbose progress information while designing with spuriousC
Ex:
$ pepper-design-spurious -v circuit -
finish.py can output a list of “strands to order”
Ex:
$ pepper-finish --strands=circuit.strands circuit
Furthermore, all input and output files can be specified specifically with options. Therefore, for example, you can run two designs on the same system at the same time. Ex:
$ pepper-compiler --output=run1.des --save=run1.save examples/Georg_System/Circuit
$ pepper-compiler --output=run2.des --save=run2.save examples/Georg_System/Circuit
(These two designs will not interfere with each other.)
The “examples/” directory has some instructive examples.
- examples/system1/ - Really simple dummy system without parametrization
- examples/system2/ - Same example, with parametrization
- examples/Georg_System/ - Georg's original logic circuit (Nature 2006)
- examples/Lulu/ - Some mock-ups of Lulu's seesaw systems
- examples/Elisa/ - Self-activating and self-inhibiting transcriptional systems
The specifications for system and component files can be found on the doc folder:
- Problems with spuriousSSM not always being installed properly by pip have been fixed.
- Fixed sequences that are not used in the system now result in a warning, rather than a cryptic error.
- Failures of SpuriousSSM should now be caught and result in more useful error messages.
- A typo in the spuriousSSM energetics parameters has been fixed.
- Added
dg=option to spuriousSSM, allowing target dGs for specified parts of sequences.